He was honorary fellow of the British Psychological Society and an honorary member of the Indian Psychological Association, he was president of the Programme Committee of the International Congress on Mental Health in 1948 and president of the psychology section of the British Medical Association in 1950.
Flügel was honorary secretary of the British Psychological Society from 1911 to 1920, honorary librarian from 1911 to 1932, and its president from 1932 to 1935. During the First World War he made a number of important contributions to the society.